NM_175856.5:c.1086+15107G>A

Variant names:

• chr5-129923467-G-A
• rs244745
• NM_175856.5:c.1086+15107G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175856.5(CHSY3):​c.1086+15107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,606 control chromosomes in the GnomAD database, including 9,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (9375 hom., cov: 30)
• Consequence: CHSY3 NM_175856.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 2 publications found

Genes affected

CHSY3 (HGNC:24293): (chondroitin sulfate synthase 3) CSS3 is a glycosyltransferase that has both glucuronyltransferase and N-acetylgalactosaminyltransferase activities (Yada et al., 2003 [PubMed 12907687]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175856.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHSY3	NM_175856.5	MANE Select	c.1086+15107G>A		intron	N/A	NP_787052.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHSY3	ENST00000305031.5	TSL:1 MANE Select	c.1086+15107G>A		intron	N/A	ENSP00000302629.4
	CHSY3	ENST00000507545.1	TSL:3	n.274+15107G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52836 AN: 151488 Hom.: 9364 Cov.: 30

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.354

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.349 AC: 52873 AN: 151606 Hom.: 9375 Cov.: 30 AF XY: 0.357 AC XY: 26439 AN XY: 74068

African (AFR) AF: 0.277 AC: 11421 AN: 41294

American (AMR) AF: 0.394 AC: 6000 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1131 AN: 3462

East Asian (EAS) AF: 0.419 AC: 2156 AN: 5146

South Asian (SAS) AF: 0.460 AC: 2207 AN: 4798

European-Finnish (FIN) AF: 0.449 AC: 4707 AN: 10476

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24124 AN: 67898

Other (OTH) AF: 0.352 AC: 741 AN: 2104

Alfa AF: 0.349 Hom.: 1295

Bravo AF: 0.339

Asia WGS AF: 0.449 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs244745; hg19: chr5-129259160; COSMIC: COSV59274281;